Sugarbeet roots are subject to tremendous physiological stress at harvest as defoliation and extraction from the soil removes roots from their source of photosynthate, water, and nutrients, and harvest and piling operations inflict injuries to roots. Roots additionally encounter environmental stress during storage from declining and fluctuating temperature and humidity conditions within piles. The physiological and environmental stresses of harvest and storage are certain to affect sugarbeet root postharvest metabolism as well as impact sugarbeet root storage properties, processing properties and sucrose yield after storage. However, the molecular changes occurring in postharvest sugarbeet roots and their relationship to root storage and processing properties are largely unknown. To better understand the molecular events occurring after harvest and their relationship to storage and processing losses, genes and metabolites that were altered in expression or concentration in roots stored at 5 and 12°C for 12, 40 and 120 days were determined and correlated to changes in root storage and processing properties. RNA sequencing and HPLC-MS analysis identified 8656 genes and 225 metabolites that were altered in expression or concentration at one or more time points during the 120 day storage period, at one or both storage temperatures. Functional annotation and pathway analysis indicated that differentially expressed genes and metabolites contributed to a diverse array of regulatory, structural and metabolic pathways, while correlation analysis identified genes and metabolites that exhibited positive or negative relationships in their expression or concentration with the deterioration in root storage and processing properties. Overall, the research indicates that a major reorientation of metabolism occurs after harvest and throughout storage and identifies genes and metabolic pathways that potentially contribute to storage losses.